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arq5x / poretools

a toolkit for working with Oxford nanopore data
MIT License
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Occupancy plot thowing an AttributeError... #149

Open nickschurch opened 7 years ago

nickschurch commented 7 years ago

Trying to make an occupancy plot with some recent MINIon DSR data I get the following error:

 > poretools occupancy mydata/fast5
channel_number  start_time  duration
Traceback (most recent call last):
  File "/sw/opt/python/2.7.12/bin/poretools", line 11, in <module>
    load_entry_point('poretools==0.6.0', 'console_scripts', 'poretools')()
  File "/cluster/gjb_lab/nschurch/.local/lib/python2.7/site-packages/poretools-0.6.0-py2.7.egg/poretools/poretools_main.py", line 538, in main
    args.func(parser, args)
  File "/cluster/gjb_lab/nschurch/.local/lib/python2.7/site-packages/poretools-0.6.0-py2.7.egg/poretools/poretools_main.py", line 55, in run_subtool
    submodule.run(parser, args)
  File "/cluster/gjb_lab/nschurch/.local/lib/python2.7/site-packages/poretools-0.6.0-py2.7.egg/poretools/occupancy.py", line 71, in run
    tot_bp_per_pore[int(pore_id)] += len(fq.seq)
AttributeError: 'NoneType' object has no attribute 'seq'

poretools 0.6.0, python 2.7.12, centos 6

tanaes commented 7 years ago

I find that I must supply a specific subfolder with this command, e.g. poretools occupancy mydata/fast5/pass.